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Feature/mouse #53

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merged 13 commits into from
Apr 4, 2020
Merged

Feature/mouse #53

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4fcfc8a
v1.2.4
marcmaxson Mar 3, 2020
ed823c6
v1.2.4 tweaks
marcmaxson Mar 10, 2020
af7ef70
unit testing
marcmaxson Mar 10, 2020
901d864
unit test fix
marcmaxson Mar 10, 2020
f3f0f9d
Merge branch 'master' into dev
Mar 10, 2020
e323e4a
readthedocs fix
marcmaxson Mar 11, 2020
9d9d3c8
Merge branch 'dev' of https://github.com/LifeEGX/methylprep into dev
marcmaxson Mar 11, 2020
2c47ade
better readthedocs autosummary
marcmaxson Mar 11, 2020
a7f35bd
pval probe detection
marcmaxson Mar 26, 2020
fa7218f
mouse array working (RND1) except for 940 failed probes
marcmaxson Mar 28, 2020
3d39c3c
fixed pval probe detection bug where manifest and idat probe names do…
marcmaxson Apr 3, 2020
ed50225
one test failed; fixed snp + control probe case in probes.py
marcmaxson Apr 3, 2020
fc9b573
Merge branch 'master' into feature/mouse
Apr 3, 2020
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unit test fix
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@marcmaxson
marcmaxson committed Mar 10, 2020
commit 901d86497f5671c55f163b3e22d9abb60992ec12
17 changes: 9 additions & 8 deletions tests/processing/test_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -61,14 +61,15 @@ def test_run_pipeline_demo_containers():
@staticmethod
def test_run_pipeline_with_create_sample_sheet():
test_data_dir = 'docs/example_data/epic_plus'
testargs = ["__program__", '-d', test_data_dir, '--no_export', '--sample_name', 'Sample_1', '--no_sample_sheet']
with patch.object(sys, 'argv', testargs):
test_data_containers = pipeline.run_pipeline(test_data_dir)
# spot checking the output.
if not test_data_containers[1].unmethylated.data_frame.iloc[0]['mean_value'] == 2712:
raise AssertionError()
if not np.isclose(test_data_containers[1].unmethylated.data_frame.iloc[0]['noob'], 4479.96501260212):
raise AssertionError()
#testargs = ["__program__", '-d', test_data_dir, '--no_export', '--sample_name', 'Sample_1', '--no_sample_sheet']
#with patch.object(sys, 'argv', testargs):
test_data_containers = pipeline.run_pipeline(test_data_dir, export=False, sample_name=['Sample_1'],
meta_data_frame=False, make_sample_sheet=True)
# spot checking the output.
if not np.isclose(test_data_containers[0]._SampleDataContainer__data_frame.iloc[0]['noob_meth'], 1180.23):
raise AssertionError()
if not np.isclose(test_data_containers[0]._SampleDataContainer__data_frame.iloc[0]['beta_value'], 0.75902253):
raise AssertionError()

@staticmethod
def test_download_manifest_dummy_file():
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